/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ext.rbvi.chimera;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.MappedFeatures;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
import jalview.util.ColorUtils;
-import jalview.util.Comparison;
+import jalview.util.StructureCommands;
import java.awt.Color;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
-import java.util.TreeMap;
/**
* Routines for generating Chimera commands for Jalview/Chimera binding
* @author JimP
*
*/
-public class ChimeraCommands
+public class ChimeraCommands extends StructureCommands
{
+ public static final String NAMESPACE_PREFIX = "jv_";
+
+ /*
+ * colour for residues shown in structure but hidden in alignment
+ */
+ private static final String COLOR_GRAY_HEX = "color "
+ + ColorUtils.toTkCode(Color.GRAY);
/**
- * utility to construct the commands to colour chains by the given alignment
- * for passing to Chimera
- *
- * @returns Object[] { Object[] { <model being coloured>,
+ * Constructs Chimera commands to colour residues as per the Jalview alignment
*
+ * @param colourMap
+ * @param binding
+ * @return
*/
- public static StructureMappingcommandSet[] getColourBySequenceCommand(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ public static String[] getColourBySequenceCommand(
+ Map<Object, AtomSpecModel> colourMap,
+ AAStructureBindingModel binding)
{
- Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap = buildColoursMap(
- ssm, files, sequence, sr, fr, alignment);
+ List<String> colourCommands = buildColourCommands(colourMap, binding);
- List<String> colourCommands = buildColourCommands(colourMap);
-
- StructureMappingcommandSet cs = new StructureMappingcommandSet(
- ChimeraCommands.class, null,
- colourCommands.toArray(new String[0]));
-
- return new StructureMappingcommandSet[] { cs };
+ return colourCommands.toArray(new String[colourCommands.size()]);
}
/**
* 'color' commands (one per distinct colour used). The format of each command
* is
*
- * <blockquote> color colorname #modelnumber:range.chain e.g. color #00ff00
- * #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
- *
- * @see http
- * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec
- * .html </pre>
+ * <pre>
+ * <blockquote>
+ * color colorname #modelnumber:range.chain
+ * e.g. color #00ff00 #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+ * </blockquote>
+ * </pre>
*
* @param colourMap
+ * @param binding
* @return
*/
protected static List<String> buildColourCommands(
- Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap)
+ Map<Object, AtomSpecModel> colourMap,
+ AAStructureBindingModel binding)
{
/*
* This version concatenates all commands into a single String (semi-colon
* delimited). If length limit issues arise, refactor to return one color
* command per colour.
*/
- List<String> commands = new ArrayList<String>();
+ List<String> commands = new ArrayList<>();
StringBuilder sb = new StringBuilder(256);
- boolean firstColour = true;
- for (Color colour : colourMap.keySet())
+ sb.append(COLOR_GRAY_HEX);
+
+ for (Object key : colourMap.keySet())
{
+ Color colour = (Color) key;
String colourCode = ColorUtils.toTkCode(colour);
- if (!firstColour)
+ sb.append("; ");
+ sb.append("color ").append(colourCode).append(" ");
+ final AtomSpecModel colourData = colourMap.get(colour);
+ sb.append(getAtomSpec(colourData, binding));
+ }
+ commands.add(sb.toString());
+ return commands;
+ }
+
+ /**
+ * Constructs and returns Chimera commands to set attributes on residues
+ * corresponding to features in Jalview. Attribute names are the Jalview feature
+ * type, with a "jv_" prefix.
+ *
+ * @param ssm
+ * @param files
+ * @param seqs
+ * @param viewPanel
+ * @param binding
+ * @return
+ */
+ public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
+ AlignmentViewPanel viewPanel, AAStructureBindingModel binding)
+ {
+ StructureSelectionManager ssm = binding.getSsm();
+ String[] files = binding.getStructureFiles();
+ SequenceI[][] seqs = binding.getSequence();
+
+ Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
+ ssm, files, seqs, viewPanel);
+
+ List<String> commands = buildSetAttributeCommands(featureMap, binding);
+
+ StructureMappingcommandSet cs = new StructureMappingcommandSet(
+ ChimeraCommands.class, null,
+ commands.toArray(new String[commands.size()]));
+
+ return cs;
+ }
+
+ /**
+ * <pre>
+ * Helper method to build a map of
+ * { featureType, { feature value, AtomSpecModel } }
+ * </pre>
+ *
+ * @param ssm
+ * @param files
+ * @param seqs
+ * @param viewPanel
+ * @return
+ */
+ protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
+ StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
+ AlignmentViewPanel viewPanel)
+ {
+ Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<>();
+
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ if (fr == null)
+ {
+ return theMap;
+ }
+
+ AlignViewportI viewport = viewPanel.getAlignViewport();
+ List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
+
+ /*
+ * if alignment is showing features from complement, we also transfer
+ * these features to the corresponding mapped structure residues
+ */
+ boolean showLinkedFeatures = viewport.isShowComplementFeatures();
+ List<String> complementFeatures = new ArrayList<>();
+ FeatureRenderer complementRenderer = null;
+ if (showLinkedFeatures)
+ {
+ AlignViewportI comp = fr.getViewport().getCodingComplement();
+ if (comp != null)
{
- sb.append("; ");
+ complementRenderer = Desktop.getAlignFrameFor(comp)
+ .getFeatureRenderer();
+ complementFeatures = complementRenderer.getDisplayedFeatureTypes();
}
- sb.append("color ").append(colourCode).append(" ");
- firstColour = false;
- boolean firstModelForColour = true;
- final Map<Integer, Map<String, List<int[]>>> colourData = colourMap
- .get(colour);
- for (Integer model : colourData.keySet())
+ }
+ if (visibleFeatures.isEmpty() && complementFeatures.isEmpty())
+ {
+ return theMap;
+ }
+
+ AlignmentI alignment = viewPanel.getAlignment();
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+
+ if (mapping == null || mapping.length < 1)
{
- boolean firstPositionForModel = true;
- if (!firstModelForColour)
+ continue;
+ }
+
+ for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++)
+ {
+ for (int m = 0; m < mapping.length; m++)
{
- sb.append("|");
+ final SequenceI seq = seqs[pdbfnum][seqNo];
+ int sp = alignment.findIndex(seq);
+ StructureMapping structureMapping = mapping[m];
+ if (structureMapping.getSequence() == seq && sp > -1)
+ {
+ /*
+ * found a sequence with a mapping to a structure;
+ * now scan its features
+ */
+ if (!visibleFeatures.isEmpty())
+ {
+ scanSequenceFeatures(visibleFeatures, structureMapping, seq,
+ theMap, pdbfnum);
+ }
+ if (showLinkedFeatures)
+ {
+ scanComplementFeatures(complementRenderer, structureMapping,
+ seq, theMap, pdbfnum);
+ }
+ }
}
- firstModelForColour = false;
- sb.append("#").append(model).append(":");
+ }
+ }
+ return theMap;
+ }
- final Map<String, List<int[]>> modelData = colourData.get(model);
- for (String chain : modelData.keySet())
+ /**
+ * Scans visible features in mapped positions of the CDS/peptide complement, and
+ * adds any found to the map of attribute values/structure positions
+ *
+ * @param complementRenderer
+ * @param structureMapping
+ * @param seq
+ * @param theMap
+ * @param modelNumber
+ */
+ protected static void scanComplementFeatures(
+ FeatureRenderer complementRenderer,
+ StructureMapping structureMapping, SequenceI seq,
+ Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
+ {
+ /*
+ * for each sequence residue mapped to a structure position...
+ */
+ for (int seqPos : structureMapping.getMapping().keySet())
+ {
+ /*
+ * find visible complementary features at mapped position(s)
+ */
+ MappedFeatures mf = complementRenderer
+ .findComplementFeaturesAtResidue(seq, seqPos);
+ if (mf != null)
+ {
+ for (SequenceFeature sf : mf.features)
{
- boolean hasChain = !"".equals(chain.trim());
- for (int[] range : modelData.get(chain))
+ String type = sf.getType();
+
+ /*
+ * Don't copy features which originated from Chimera
+ */
+ if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
+ .equals(sf.getFeatureGroup()))
{
- if (!firstPositionForModel)
+ continue;
+ }
+
+ /*
+ * record feature 'value' (score/description/type) as at the
+ * corresponding structure position
+ */
+ List<int[]> mappedRanges = structureMapping
+ .getPDBResNumRanges(seqPos, seqPos);
+
+ if (!mappedRanges.isEmpty())
+ {
+ String value = sf.getDescription();
+ if (value == null || value.length() == 0)
{
- sb.append(",");
+ value = type;
}
- if (range[0] == range[1])
+ float score = sf.getScore();
+ if (score != 0f && !Float.isNaN(score))
{
- sb.append(range[0]);
+ value = Float.toString(score);
}
- else
+ Map<Object, AtomSpecModel> featureValues = theMap.get(type);
+ if (featureValues == null)
{
- sb.append(range[0]).append("-").append(range[1]);
+ featureValues = new HashMap<>();
+ theMap.put(type, featureValues);
}
- if (hasChain)
+ for (int[] range : mappedRanges)
{
- sb.append(".").append(chain);
+ addAtomSpecRange(featureValues, value, modelNumber, range[0],
+ range[1], structureMapping.getChain());
}
- firstPositionForModel = false;
}
}
}
}
- commands.add(sb.toString());
- return commands;
}
/**
- * <pre>
- * Build a data structure which maps contiguous subsequences for each colour.
- * This generates a data structure from which we can easily generate the
- * Chimera command for colour by sequence.
- * Color
- * Model number
- * Chain
- * list of start/end ranges
- * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
- * </pre>
+ * Inspect features on the sequence; for each feature that is visible, determine
+ * its mapped ranges in the structure (if any) according to the given mapping,
+ * and add them to the map.
+ *
+ * @param visibleFeatures
+ * @param mapping
+ * @param seq
+ * @param theMap
+ * @param modelNumber
*/
- protected static Map<Color, Map<Integer, Map<String, List<int[]>>>> buildColoursMap(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ protected static void scanSequenceFeatures(List<String> visibleFeatures,
+ StructureMapping mapping, SequenceI seq,
+ Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
{
- Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap = new LinkedHashMap<Color, Map<Integer, Map<String, List<int[]>>>>();
- Color lastColour = null;
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures(
+ visibleFeatures.toArray(new String[visibleFeatures.size()]));
+ for (SequenceFeature sf : sfs)
{
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+ String type = sf.getType();
- if (mapping == null || mapping.length < 1)
+ /*
+ * Don't copy features which originated from Chimera
+ */
+ if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
+ .equals(sf.getFeatureGroup()))
{
continue;
}
- int startPos = -1, lastPos = -1;
- String lastChain = "";
- for (int s = 0; s < sequence[pdbfnum].length; s++)
+ List<int[]> mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(),
+ sf.getEnd());
+
+ if (!mappedRanges.isEmpty())
{
- for (int sp, m = 0; m < mapping.length; m++)
+ String value = sf.getDescription();
+ if (value == null || value.length() == 0)
{
- final SequenceI seq = sequence[pdbfnum][s];
- if (mapping[m].getSequence() == seq
- && (sp = alignment.findIndex(seq)) > -1)
- {
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // no mapping to gaps in sequence
- if (Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- {
- continue;
- }
-
- Color colour = sr.getResidueColour(seq, r, fr);
- final String chain = mapping[m].getChain();
-
- /*
- * Just keep incrementing the end position for this colour range
- * _unless_ colour, PDB model or chain has changed, or there is a
- * gap in the mapped residue sequence
- */
- final boolean newColour = !colour.equals(lastColour);
- final boolean nonContig = lastPos + 1 != pos;
- final boolean newChain = !chain.equals(lastChain);
- if (newColour || nonContig || newChain)
- {
- if (startPos != -1)
- {
- addColourRange(colourMap, lastColour, pdbfnum, startPos,
- lastPos, lastChain);
- }
- startPos = pos;
- }
- lastColour = colour;
- lastPos = pos;
- lastChain = chain;
- }
- // final colour range
- if (lastColour != null)
- {
- addColourRange(colourMap, lastColour, pdbfnum, startPos,
- lastPos, lastChain);
- }
- break;
- }
+ value = type;
+ }
+ float score = sf.getScore();
+ if (score != 0f && !Float.isNaN(score))
+ {
+ value = Float.toString(score);
+ }
+ Map<Object, AtomSpecModel> featureValues = theMap.get(type);
+ if (featureValues == null)
+ {
+ featureValues = new HashMap<>();
+ theMap.put(type, featureValues);
+ }
+ for (int[] range : mappedRanges)
+ {
+ addAtomSpecRange(featureValues, value, modelNumber, range[0],
+ range[1], mapping.getChain());
}
}
}
- return colourMap;
}
/**
- * Helper method to add one contiguous colour range to the colour map.
+ * Traverse the map of features/values/models/chains/positions to construct a
+ * list of 'setattr' commands (one per distinct feature type and value).
+ * <p>
+ * The format of each command is
*
- * @param colourMap
- * @param colour
- * @param model
- * @param startPos
- * @param endPos
- * @param chain
+ * <pre>
+ * <blockquote> setattr r <featureName> " " #modelnumber:range.chain
+ * e.g. setattr r jv:chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+ * </blockquote>
+ * </pre>
+ *
+ * @param featureMap
+ * @param binding
+ * @return
*/
- protected static void addColourRange(
- Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap,
- Color colour, int model, int startPos, int endPos, String chain)
+ protected static List<String> buildSetAttributeCommands(
+ Map<String, Map<Object, AtomSpecModel>> featureMap,
+ AAStructureBindingModel binding)
{
- /*
- * Get/initialize map of data for the colour
- */
- Map<Integer, Map<String, List<int[]>>> colourData = colourMap
- .get(colour);
- if (colourData == null)
+ List<String> commands = new ArrayList<>();
+ for (String featureType : featureMap.keySet())
{
- colourMap
- .put(colour,
- colourData = new TreeMap<Integer, Map<String, List<int[]>>>());
+ String attributeName = makeAttributeName(featureType);
+
+ /*
+ * clear down existing attributes for this feature
+ */
+ // 'problem' - sets attribute to None on all residues - overkill?
+ // commands.add("~setattr r " + attributeName + " :*");
+
+ Map<Object, AtomSpecModel> values = featureMap.get(featureType);
+ for (Object value : values.keySet())
+ {
+ /*
+ * for each distinct value recorded for this feature type,
+ * add a command to set the attribute on the mapped residues
+ * Put values in single quotes, encoding any embedded single quotes
+ */
+ StringBuilder sb = new StringBuilder(128);
+ String featureValue = value.toString();
+ featureValue = featureValue.replaceAll("\\'", "'");
+ sb.append("setattr r ").append(attributeName).append(" '")
+ .append(featureValue).append("' ");
+ sb.append(getAtomSpec(values.get(value), binding));
+ commands.add(sb.toString());
+ }
}
- /*
- * Get/initialize map of data for the colour and model
- */
- Map<String, List<int[]>> modelData = colourData.get(model);
- if (modelData == null)
+ return commands;
+ }
+
+ /**
+ * Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied
+ * for a 'Jalview' namespace, and any non-alphanumeric character is converted
+ * to an underscore.
+ *
+ * @param featureType
+ * @return
+ *
+ * <pre>
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
+ * </pre>
+ */
+ protected static String makeAttributeName(String featureType)
+ {
+ StringBuilder sb = new StringBuilder();
+ if (featureType != null)
{
- colourData.put(model, modelData = new TreeMap<String, List<int[]>>());
+ for (char c : featureType.toCharArray())
+ {
+ sb.append(Character.isLetterOrDigit(c) ? c : '_');
+ }
}
+ String attName = NAMESPACE_PREFIX + sb.toString();
/*
- * Get/initialize map of data for colour, model and chain
+ * Chimera treats an attribute name ending in 'color' as colour-valued;
+ * Jalview doesn't, so prevent this by appending an underscore
*/
- List<int[]> chainData = modelData.get(chain);
- if (chainData == null)
+ if (attName.toUpperCase().endsWith("COLOR"))
{
- modelData.put(chain, chainData = new ArrayList<int[]>());
+ attName += "_";
}
- /*
- * Add the start/end positions
- */
- chainData.add(new int[] { startPos, endPos });
+ return attName;
+ }
+
+ /**
+ * Returns the range(s) formatted as a Chimera atomspec
+ *
+ * @return
+ */
+ public static String getAtomSpec(AtomSpecModel atomSpec,
+ AAStructureBindingModel binding)
+ {
+ StringBuilder sb = new StringBuilder(128);
+ boolean firstModel = true;
+ for (Integer model : atomSpec.getModels())
+ {
+ if (!firstModel)
+ {
+ sb.append("|");
+ }
+ firstModel = false;
+ sb.append(binding.getModelSpec(model)).append(":");
+
+ boolean firstPositionForModel = true;
+
+ for (String chain : atomSpec.getChains(model))
+ {
+ chain = " ".equals(chain) ? chain : chain.trim();
+
+ List<int[]> rangeList = atomSpec.getRanges(model, chain);
+
+ String chainToken = " ".equals(chain) ? "." : "." + chain;
+ appendResidueRange(sb, rangeList, chainToken,
+ firstPositionForModel);
+ firstPositionForModel = false;
+ }
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Chimera atomspec requires chain to be specified for each start-end residue
+ * range, otherwise it will apply to all chains
+ *
+ * @param sb
+ * @param chain
+ */
+ protected static void appendChainToRange(StringBuilder sb, String chain)
+ {
+ sb.append(".");
+ if (!" ".equals(chain))
+ {
+ sb.append(chain);
+ }
}
}